Results for the regional assessment (PhD Chapter 1)
Section 1/2
This series of files compile all analyses done during Chapter 1 for the regional assessment (Campaign 2016).
- Section 1 regroups maps, graphical ordinations and clustering.
- Section 2 presents SIMPER and regressions results.
All analyses have been done with PRIMER-e 6 and R 3.6.0.
Caracteristics of each campaign
| 2014 | 2016 | 2017 | ||
|---|---|---|---|---|
| Sampling date | August-September | June to August | July | |
| Criteria for perturbation | Potentially impacted if close to the city or industries, References outside the bay | Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria | Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria | |
| Regions considered | BSI | BSI, CPC, BDA, MR | BSI, MR | |
| Number of sampled stations | 40 (20 HI, 20 R) | 78 (26 BSI, 19 CPC, 18 BDA, 15 MR) | 126 (111 BSI, 15 MR) | |
| Parameters sampled | Organic matter | yes | yes | yes |
| Photosynthetic pigments | no | yes | yes | |
| Sediment grain-size | yes | yes | yes | |
| Heavy-metals | yes | yes (for a limited number of stations) | no (interpolated based on 2014 and 2016 values) | |
| Benthic communities | Compartment targeted | Macro-infauna | Macro-infauna | Macro-infauna |
| Sieved used | 500 µm | 1 mm | 500 µm and 1 mm | |
| Conservation technique | Formaldehyle | Formaldehyle | Formaldehyle | |
| Others | N.A. | N.A. | N.A. |
Click on the table of contents in the left margin to assess a specific analysis
Click on a figure to zoom it
To assess Section 2, click here.
To go back to the summary page, click here.
We selected variables and characteristic species (using IndVal index and SIMPER procedure, see Section 2) for the analyses:
- Depth of the station: depth
- Percentage of organic matter: om
- Percentage of gravel: gravel
- Percentage of sand: sand
- Percentage of silt: silt
- Percentage of clay: clay
- Concentration of arsenic: arsenic
- Concentration of cadmium: cadmium
- Concentration of chromium: chromium
- Concentration of copper: copper
- Concentration of iron: iron
- Concentration of manganese: manganese
- Concentration of mercury: mercury
- Concentration of lead: lead
- Concentration of zinc: zinc
- Species richness: S
- Abundance of total individuals: N
- Shannon index: H
- Piélou evenness: J
- Abundance of Mesodesma arctatum: Marc
- Abundance of Cistenides granulata: Cgra
As there is missing data for metal concentrations outside BSI, two Designs have been used:
- Design 1: stations at BSI, CPC, BDA, MR with only habitat parameters
- Design 2: stations at BSI with habitat parameters and heavy metal concentrations.
Workspace preparation
# library(clustsig)
library(dendextend)
library(FactoMineR)
library(graphicsutils)
library(pander)
library(plotrix)
library(RColorBrewer)
library(reshape2)
library(sf)
library(stats)
library(tidyverse)
library(vegan)Here, we use data from subtidal ecosystems (see metadata files for more information)
Only stations that have been sampled both for abiotic parameters and benthic species were included.
The script below includes personnal functions, refined data, parameters for each campaign and global means, sd, se.
Maps
1. General map
2. Parameters maps
For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity.
OM
Gravel
Sand
Silt
Clay
Arsenic
Cadmium
Chromium
Copper
Iron
Manganese
Mercury
Lead
Zinc
Cgra
Marc
Epar
Species richness
Total abundance
Shannon index
Piélou’s evenness
Analyses
1. Barplots
Depth
Organic matter
Grain-size
Heavy metals
This section is not relevant here, as we only have data for BSI.
Species abundances
Diversity indices
2. Phylum frequencies
| Phylum | BSI | CPC | BDA | MR |
|---|---|---|---|---|
| Annelida | 214 | 69 | 188 | 43 |
| Mollusca | 191 | 45 | 89 | 100 |
| Arthropoda | 119 | 13 | 30 | 43 |
| Echinodermata | 27 | 206 | 24 | 138 |
| Platyhelminthes | 3 | 0 | 0 | 0 |
| Nematoda | 2 | 0 | 0 | 0 |
| Nemertea | 1 | 0 | 0 | 0 |
| Brachiopoda | 0 | 0 | 0 | 2 |
| Cnidaria | 0 | 0 | 0 | 1 |
| Hemichordata | 0 | 0 | 0 | 0 |
| Phoronida | 0 | 0 | 0 | 0 |
| Sipuncula | 0 | 0 | 0 | 0 |
3. Species estimation curves
4. Principal Component Analysis
Design 1
Variables have been scaled by mean and standard-deviation prior to analysis.
Design 2
Variables have been scaled by mean and standard-deviation prior to analysis.
Metals at BSI
Variables have been scaled by mean and standard-deviation prior to analysis.
5. Non-metric Multidimensional Scaling
Design 1
Variables have been scaled by mean and standard-deviation prior to analysis.
Design 2
Variables have been scaled by mean and standard-deviation prior to analysis.
Metals at BSI
Variables have been scaled by mean and standard-deviation prior to analysis.
Species
Stations with no species are deleted from this analysis.
6. Hierarchical Agglomerative Clustering
Design 1
Variables have been scaled by mean and standard-deviation prior to analysis.
## 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61
## 1 2 2 2 2 2 2 2 2 2 3 3 1 3 1 1 3 2
## 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79
## 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 2 2 2
## 80 82 83 86 87 88 90 92 93 94 95 96 97 98 99 100 101 102
## 3 3 3 2 2 2 3 1 1 1 1 3 1 3 1 1 3 2
## 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
## 3 3 1 2 1 3 2 2 3 2 2 1 1 3 3 3 1 2
## 121 122 123 124 125 126
## 1 1 3 3 1 1
Design 2
Variables have been scaled by mean and standard-deviation prior to analysis.
## 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118
## 1 2 1 1 2 2 2 1 2 2 3 2 2 3 2 3 3 3
## 119 120 121 122 123 124 125 126
## 3 2 2 2 3 3 3 2
Metals at BSI
Variables have been scaled by mean and standard-deviation prior to analysis.
## 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118
## 1 2 1 1 3 3 3 1 3 3 3 3 3 3 3 3 2 2
## 119 120 121 122 123 124 125 126
## 3 3 3 3 3 2 3 3
Species
Stations with no species are deleted from this analysis.
## 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61
## 1 1 1 1 1 1 1 1 1 2 1 1 3 1 2 2 1 2
## 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79
## 2 2 1 1 1 1 3 1 2 2 1 1 2 2 1 1 2 2
## 82 83 86 87 90 92 93 94 95 96 97 98 99 100 101 102 103 104
## 1 3 1 2 1 2 3 3 1 1 3 1 3 3 1 1 1 1
## 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122
## 1 1 1 1 1 1 1 3 1 3 1 1 1 1 1 2 1 3
## 123 124 125 126
## 1 1 1 1
To assess Section 2, click here.
To go back to Chapter 1’s index page, click here.